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add more LGG tumors (#110)
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* add more LGG tumors

* fix valid values
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@allaway
allaway authored Feb 13, 2022
1 parent 6c8eec6 commit d1c8d54
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8 changes: 6 additions & 2 deletions NF.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -87,7 +87,7 @@ Short Tau Inversion Recovery,,,,FALSE,Sage Bionetworks,MRISequence,,,,Short_Tau_
head,The head is the anterior-most division of the body.,,,FALSE,http://purl.obolibrary.org/obo/UBERON_0000033,bodyPart,,,,Head,Class,Body_Part,Body_Part,,,
transplantationType,"Type of transplantation involved in the experiment, derived from MESH","allograft, xenograft, autograft, isograft",,FALSE,,cancer,,,,transplantationType,Property,experimentAnnotation,transplantationCharacteristic,,,
transplantationRecipientSpecies,Species into which donor tissue was grown,"Human, Mouse",,FALSE,,cancer,,,,transplantationRecipientSpecies,Property,experimentAnnotation,transplantationCharacteristic,,,
tumorType,The type of tumor that the biospecimen used to generate the data were collected from. ,"Cutaneous Neurofibroma, Plexiform Neurofibroma, Atypical Neurofibroma, Malignant Peripheral Nerve Sheath Tumor, Glioma, Low Grade Glioma, Diffuse Astrocytoma, Anaplastic Astrocytoma, Glioblastoma, Schwannoma, Meningioma, normal, Teratoma, Massive Soft Tissue Neurofibroma, Diffuse Infiltrating Neurofibroma, Localized Neurofibroma, Neurofibroma, Neurofibroma with Degenerative Atypia, Low-Grade Glioma NOS, Pilocytic Astrocytoma, Pilomyxoid Astrocytoma, Diffuse Astrocytoma, Glioblastoma Multiforme, Anaplastic Pilocytic Astrocytoma, Pleomorphic Xanthoastrocytoma, Oligoastrocytoma, High-Grade Glioma NOS, Unknown",,FALSE,Sage Bionetworks [RJA],cancer,,,,tumorType,Property,annotationProperty,biosampleAnnotation,Tumor,,
tumorType,The type of tumor that the biospecimen used to generate the data were collected from. ,"Teratoma, Cutaneous Neurofibroma, Plexiform Neurofibroma, Atypical Neurofibroma, Malignant Peripheral Nerve Sheath Tumor, Glioma, Low-Grade Glioma NOS, Pilocytic Astrocytoma, Pilomyxoid Astrocytoma, Diffuse Astrocytoma, Glioblastoma Multiforme, Anaplastic Pilocytic Astrocytoma, Pleomorphic Xanthoastrocytoma, Oligoastrocytoma, High-Grade Glioma NOS, Unknown, Anaplastic Astrocytoma, Glioblastoma, Schwannoma, Meningioma, Massive Soft Tissue Neurofibroma, Diffuse Infiltrating Neurofibroma, Localized Neurofibroma, Neurofibroma with Degenerative Atypia, Neurofibroma, Anaplastic Pleomorphic Xanthoastrocytoma, Ganglioglioma, Anaplastic Ganglioglioma, Optic Pathway Glioma, Not Applicable",,FALSE,Sage Bionetworks,cancer,,,,tumorType,Property,annotationProperty,biosampleAnnotation,Tumor,,
genePerturbationType,Specific way in which a single gene was perturbed in a sample,"overexpression, knockdown, knockout, Not Applicable",genePerturbationTechnology,FALSE,,cancer,,,,genePerturbationType,Property,,,Gene_Perturbation,,
genePerturbationTechnology,Technology used to perform gene perturbation,"RNAi, CRISPR, CRE Recombinase",,FALSE,,cancer,,,,genePerturbationTechnology,Property,,,Gene_Perturbation_Technology,,
timePointUnit,For timed experiments this represents the unit of time measured,"seconds, minutes, hours, days, weeks, months, quarters",,FALSE,,cancer,,,,timePointUnit,Property,,,Time_Unit,,
Expand Down Expand Up @@ -584,7 +584,11 @@ Massive Soft Tissue Neurofibroma,"Massive soft tissue neurofibroma is characteri
Diffuse Infiltrating Neurofibroma,"Diffuse infiltrating neurofibroma can present as slow-growing, soft tissue masses with overlying skin thickening. These le-sions infiltrate the dermis and the subcutaneous tissue and characteristically spread along the connective tissues enveloping islands of normal fat. Some of these lesions develop fatty proliferation and can mimic lipomas, angiolipomas, or angiomyolipomas on imaging and histological evaluation ",,,FALSE,https://doi.org/10.1007/s00256-014-1965-8,tumorType,,,,Diffuse_Infiltrating_Neurofibroma,Class,Tumor,Tumor,,,
Localized Neurofibroma,,,,FALSE,JHU Biobank,tumorType,,,,Localized_Neurofibroma,Class,Tumor,Tumor,,,
Neurofibroma with Degenerative Atypia,,,,FALSE,JHU Biobank,tumorType,,,,Neurofibroma_With_Degenerative_Atypia,Class,Tumor,Tumor,,,
Neurofibroma,NFIB,,,FALSE,ONCOTREE,tumorType,,,,Neurofibroma,Class,Tumor,Tumor,,,
Neurofibroma,NFIB,,,FALSE,,tumorType,,,,Neurofibroma,Class,Tumor,Tumor,,,
Anaplastic Pleomorphic Xanthoastrocytoma,APXA,,,FALSE,ONCOTREE,tumorType,,,,,,,,,,
Ganglioglioma,GNG,,,FALSE,ONCOTREE,tumorType,,,,,,,,,,
Anaplastic Ganglioglioma,AGNG,,,FALSE,ONCOTREE,tumorType,,,,,,,,,,
Optic Pathway Glioma,A glioma that affects the optic nerve. This condition can be seen in association with neurofibromatosis 1. It is most commonly seen in the pediatric age group. ,,,FALSE,https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=C4537,tumorType,,,,,,,,,,
Not Applicable,,,,FALSE,Sage Bionetworks,tumorType,,,,,,,,,,
PacBio Sequel IIe System,PacBio Sequel IIe System,,,,,,,,,,,,,,,
PacBio Sequel II System,PacBio Sequel II System,,,,,,,,,,,,,,,
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137 changes: 97 additions & 40 deletions NF.jsonld
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Original file line number Diff line number Diff line change
Expand Up @@ -3531,6 +3531,9 @@
"@id": "http://schema.biothings.io"
},
"schema:rangeIncludes": [
{
"@id": "bts:Teratoma"
},
{
"@id": "bts:CutaneousNeurofibroma"
},
Expand All @@ -3547,73 +3550,76 @@
"@id": "bts:Glioma"
},
{
"@id": "bts:LowGradeGlioma"
"@id": "bts:Low-GradeGliomaNOS"
},
{
"@id": "bts:DiffuseAstrocytoma"
"@id": "bts:PilocyticAstrocytoma"
},
{
"@id": "bts:AnaplasticAstrocytoma"
"@id": "bts:PilomyxoidAstrocytoma"
},
{
"@id": "bts:Glioblastoma"
"@id": "bts:DiffuseAstrocytoma"
},
{
"@id": "bts:Schwannoma"
"@id": "bts:GlioblastomaMultiforme"
},
{
"@id": "bts:Meningioma"
"@id": "bts:AnaplasticPilocyticAstrocytoma"
},
{
"@id": "bts:Normal"
"@id": "bts:PleomorphicXanthoastrocytoma"
},
{
"@id": "bts:Teratoma"
"@id": "bts:Oligoastrocytoma"
},
{
"@id": "bts:MassiveSoftTissueNeurofibroma"
"@id": "bts:High-GradeGliomaNOS"
},
{
"@id": "bts:DiffuseInfiltratingNeurofibroma"
"@id": "bts:Unknown"
},
{
"@id": "bts:LocalizedNeurofibroma"
"@id": "bts:AnaplasticAstrocytoma"
},
{
"@id": "bts:Neurofibroma"
"@id": "bts:Glioblastoma"
},
{
"@id": "bts:NeurofibromawithDegenerativeAtypia"
"@id": "bts:Schwannoma"
},
{
"@id": "bts:Low-GradeGliomaNOS"
"@id": "bts:Meningioma"
},
{
"@id": "bts:PilocyticAstrocytoma"
"@id": "bts:MassiveSoftTissueNeurofibroma"
},
{
"@id": "bts:PilomyxoidAstrocytoma"
"@id": "bts:DiffuseInfiltratingNeurofibroma"
},
{
"@id": "bts:DiffuseAstrocytoma"
"@id": "bts:LocalizedNeurofibroma"
},
{
"@id": "bts:GlioblastomaMultiforme"
"@id": "bts:NeurofibromawithDegenerativeAtypia"
},
{
"@id": "bts:AnaplasticPilocyticAstrocytoma"
"@id": "bts:Neurofibroma"
},
{
"@id": "bts:PleomorphicXanthoastrocytoma"
"@id": "bts:AnaplasticPleomorphicXanthoastrocytoma"
},
{
"@id": "bts:Oligoastrocytoma"
"@id": "bts:Ganglioglioma"
},
{
"@id": "bts:High-GradeGliomaNOS"
"@id": "bts:AnaplasticGanglioglioma"
},
{
"@id": "bts:Unknown"
"@id": "bts:OpticPathwayGlioma"
},
{
"@id": "bts:NotApplicable"
}
],
"sms:displayName": "tumorType",
Expand Down Expand Up @@ -14740,6 +14746,74 @@
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:AnaplasticPleomorphicXanthoastrocytoma",
"@type": "rdfs:Class",
"rdfs:comment": "APXA",
"rdfs:label": "AnaplasticPleomorphicXanthoastrocytoma",
"rdfs:subClassOf": [
{
"@id": "bts:TumorType"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Anaplastic Pleomorphic Xanthoastrocytoma",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:Ganglioglioma",
"@type": "rdfs:Class",
"rdfs:comment": "GNG",
"rdfs:label": "Ganglioglioma",
"rdfs:subClassOf": [
{
"@id": "bts:TumorType"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Ganglioglioma",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:AnaplasticGanglioglioma",
"@type": "rdfs:Class",
"rdfs:comment": "AGNG",
"rdfs:label": "AnaplasticGanglioglioma",
"rdfs:subClassOf": [
{
"@id": "bts:TumorType"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Anaplastic Ganglioglioma",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:OpticPathwayGlioma",
"@type": "rdfs:Class",
"rdfs:comment": "A glioma that affects the optic nerve. This condition can be seen in association with neurofibromatosis 1. It is most commonly seen in the pediatric age group. ",
"rdfs:label": "OpticPathwayGlioma",
"rdfs:subClassOf": [
{
"@id": "bts:TumorType"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Optic Pathway Glioma",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:NotApplicable",
"@type": "rdfs:Class",
Expand Down Expand Up @@ -16230,23 +16304,6 @@
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:LowGradeGlioma",
"@type": "rdfs:Class",
"rdfs:comment": "TBD",
"rdfs:label": "LowGradeGlioma",
"rdfs:subClassOf": [
{
"@id": "bts:TumorType"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "Low Grade Glioma",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:TRUE",
"@type": "rdfs:Class",
Expand Down

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